The Cell Transformation Assay: A Historical Assessment of Current Knowledge of Applications in an Integrated Approach to Testing and Assessment for Non-Genotoxic Carcinogens.

The history of the development of the cell transformation assays (CTAs) is described, providing an overview of in vitro cell transformation from its origin to the new transcriptomic-based CTAs. Application of this knowledge is utilized to address how the different types of CTAs, variously addressing initiation and promotion, can be included on a mechanistic basis within the integrated approach to testing and assessment (IATA) for non-genotoxic carcinogens. Building upon assay assessments targeting the key events in the IATA, we identify how the different CTA models can appropriately fit, following preceding steps in the IATA. The preceding steps are the prescreening transcriptomic approaches, and assessment within the earlier key events of inflammation, immune disruption, mitotic signaling and cell injury. The CTA models address the later key events of (sustained) proliferation and change in morphology leading to tumor formation. The complementary key biomarkers with respect to the precursor key events and respective CTAs are mapped, providing a structured mechanistic approach to represent the complexity of the (non-genotoxic) carcinogenesis process, and specifically their capacity to identify non-genotoxic carcinogenic chemicals in a human relevant IATA.

Detection and analysis of chemical-induced chromosomal damage for public health: integrating new approach methodologies and non-animal methods.

Chromosomal damage occurs both endogenously and exogenously and is a crucial factor in the induction of carcinogenesis. Chemically induced chromosomal damage is mainly exogenous. The OECD has developed methods to detect chemicals that induce chromosomal damage so as to identify hazardous substances and limit their exposure to humans. The development and improvement of in vitro mammalian cell methods have been the focus of recent research, as these techniques have higher throughput than in vivo animal methods and are cruelty-free. In vitro mammalian cell methods are highly sensitive and widely used. Nevertheless, they have a high frequency of misleading positive test results, causing the wastage of vital raw materials and pharmaceutical agents, and necessitating additional in vivo animal tests. Therefore, the improvement of in vitro mammalian cell methods is required. Novel methodologies have been proposed and developed for robust animal-free evaluation. As they include omics and AI approaches that use big data, they may enable objective, multidirectional interpretation when applied in combination with current in vitro experimental techniques. We review the existing approaches toward improving chromosome damage detection and introduce innovative techniques that facilitate animal-free testing. The current and latest evaluation methods can support the protection of public health as well as the development of promising chemicals that enrich our lives.

Study of spatiotemporal regulation of kinase signaling using genetically encodable molecular tools.

Precise spatiotemporal organization and regulation of signal transduction networks are essential for cellular response to internal and external cues. To understand how this biochemical activity architecture impacts cellular function, many genetically encodable tools which regulate kinase activity at a subcellular level have been developed. In this review, we highlight various types of genetically encodable molecular tools, including tools to regulate endogenous kinase activity and biorthogonal techniques to perturb kinase activity. Finally, we emphasize the use of these tools alongside biosensors for kinase activity to measure and perturb kinase activity in real time for a better understanding of the cellular biochemical activity architecture.

Evaluation of the mode of action and human relevance of liver tumors in male mice treated with epyrifenacil.

Epyrifenacil (trademark name: Rapidicil®), a novel protoporphyrinogen oxidase (PPO)-inhibiting herbicide, induces hepatocellular adenomas and carcinomas in male CD-1 mice after 78 weeks treatment. The mode of action (MOA) of these mouse liver tumors and their relevance to humans was assessed based on the 2006 International Programme on Chemical Safety (IPCS) Human Relevance Framework. Epyrifenacil is not genotoxic and induced liver tumors via the postulated porphyria-mediated cytotoxicity MOA with the following key events: (#1) PPO inhibition; (#2) porphyrin accumulation; (#3) hepatocellular injury; with (#4) subsequent regenerative cell proliferation; and ultimately (#5) development of liver tumors. This article evaluates the weight of evidence for this MOA based on the modified Bradford Hill criteria. The MOA data were aligned with the dose and temporal concordance, biological plausibility, coherence, strength, consistency, and specificity for a porphyria-mediated cytotoxicity MOA while excluding other alternative MOAs. Although the postulated MOA could qualitatively potentially occur in humans, we demonstrate that it is unlikely to occur in humans because of quantitative toxicodynamic and toxicokinetic differences between mice and humans. Therefore, this MOA is considered not relevant to humans, utilizing the IPCS Human Relevance Framework; consequently, a nonlinear, threshold dose response would be appropriate for human risk assessment.

Mechanistic Interrogation of Cell Transformation In Vitro: The Transformics Assay as an Exemplar of Oncotransformation.

The Transformics Assay is an in vitro test which combines the BALB/c 3T3 Cell Transformation Assay (CTA) with microarray transcriptomics. It has been shown to improve upon the mechanistic understanding of the CTA, helping to identify mechanisms of action leading to chemical-induced transformation thanks to RNA extractions in specific time points along the process of in vitro transformation. In this study, the lowest transforming concentration of the carcinogenic benzo(a)pyrene (B(a)P) has been tested in order to find molecular signatures of initial events relevant for oncotransformation. Application of Enrichment Analysis (Metacore) to the analyses of the results facilitated key biological interpretations. After 72 h of exposure, as a consequence of the molecular initiating event of aryl hydrocarbon receptor (AhR) activation, there is a cascade of cellular events and microenvironment modification, and the immune and inflammatory responses are the main processes involved in cell response. Furthermore, pathways and processes related to cell cycle regulation, cytoskeletal adhesion and remodeling processes, cell differentiation and transformation were observed.

Tumorigenicity risk of iPSCs in vivo: nip it in the bud.

In 2006, Takahashi and Yamanaka first created induced pluripotent stem cells from mouse fibroblasts via the retroviral introduction of genes encoding the transcription factors Oct3/4, Sox2, Klf44, and c-Myc. Since then, the future clinical application of somatic cell reprogramming technology has become an attractive research topic in the field of regenerative medicine. Of note, considerable interest has been placed in circumventing ethical issues linked to embryonic stem cell research. However, tumorigenicity, immunogenicity, and heterogeneity may hamper attempts to deploy this technology therapeutically. This review highlights the progress aimed at reducing induced pluripotent stem cells tumorigenicity risk and how to assess the safety of induced pluripotent stem cells cell therapy products.

A Novel Material for High-Performance Li-O2 Battery Separator: Polyetherketone Nanofiber Membrane.

The properties of separators significantly affect the efficiency, stability, and safety of the lithium-based batteries. Therefore, the improvement of the separator material is critical. Polyetherketone (PEK) has excellent general properties, such as mechanical strength, chemical stability, and thermal stability. Thus, it is expected to be an optimal separator material. However, its low solubility-induced poor processibility makes it difficult to be used for nanoscale product manufacturing. In this work, the soluble precursor polymer is prepared by introducing a "protecting" group into monomer, and fabricated into nanofiber membrane, which can be converted into polyetherketone nanofiber membrane by a simple acid treatment. The membrane prepared by this chemical-induced crystallization method exhibits superior chemical, thermal stability, and mechanical strength. Li-O2 batteries with the fabricated membrane as separator have a high cycling stability (194 cycles at 200 mA g-1 and 500 mAh g-1 ). This work broadens the application field of PEK and provides a potential route for battery separators.

Ammonia exposure by intratracheal instillation causes severe and deteriorating lung injury and vascular effects in mice.

OBJECTIVE: Ammonia (NH3) is a corrosive alkaline gas that can cause life-threatening injuries by inhalation. The aim was to establish a disease model for NH3-induced injuries similar to acute lung injury (ALI) described in exposed humans and investigate the progression of lung damage, respiratory dysfunction and evaluate biomarkers for ALI and inflammation over time. METHODS: Female BALB/c mice were exposed to an NH3 dose of 91.0 mg/kg·bw using intratracheal instillation and the pathological changes were followed for up to 7 days. RESULTS: NH3 instillation resulted in the loss of body weight along with a significant increase in pro-inflammatory mediators in both bronchoalveolar lavage fluid (e.g. IL-1ß, IL-6, KC, MMP-9, SP-D) and blood (e.g. IL-6, Fibrinogen, PAI-1, PF4/CXCL4, SP-D), neutrophilic lung inflammation, alveolar damage, increased peripheral airway resistance and methacholine-induced airway hyperresponsiveness compared to controls at 20 h. On day 7 after exposure, deteriorating pathological changes such as increased macrophage lung infiltration, heart weights, lung hemorrhages and coagulation abnormalities (elevated plasma levels of PAI-1, fibrinogen, endothelin and thrombomodulin) were observed but no increase in lung collagen. Some of the analyzed blood biomarkers (e.g. RAGE, IL-1ß) were unaffected despite severe ALI and may not be significant for NH3-induced damages. CONCLUSIONS: NH3 induces severe acute lung injuries that deteriorate over time and biomarkers in lungs and blood that are similar to those found in humans. Therefore, this model has potential use for developing diagnostic tools for NH3-induced ALI and for finding new therapeutic treatments, since no specific antidote has been identified yet.

Bioorthogonal Chemical Epigenetic Modifiers Enable Dose-Dependent CRISPR Targeted Gene Activation in Mammalian Cells.

CRISPR-Cas9 systems have been developed to regulate gene expression by using either fusions to epigenetic regulators or, more recently, through the use of chemically mediated strategies. These approaches have armed researchers with new tools to examine the function of proteins by intricately controlling expression levels of specific genes. Here we present a CRISPR-based chemical approach that uses a new chemical epigenetic modifier (CEM) to hone to a gene targeted with a catalytically inactive Cas9 (dCas9) bridged to an FK506-binding protein (FKBP) in mammalian cells. One arm of the bifunctional CEM recruits BRD4 to the target site, and the other arm is composed of a bumped ligand that binds to a mutant FKBP with a compensatory hole at F36V. This bump-and-hole strategy allows for activation of target genes in a dose-dependent and reversible fashion with increased specificity and high efficacy, providing a new synthetic biology approach to answer important mechanistic questions in the future.

Dataset on transcriptomic profiling of cholestatic liver injury induced by food additives and a cosmetic ingredient.

The provided dataset describes the differential gene expression profile of human hepatoma HepaRG cells cultured in monolayer configuration upon treatment with chemical compounds with cholestatic potential, including food additives sunset yellow and tartrazine and cosmetic ingredient triclosan, while being exposed to a highly concentrated bile acid mixture. Whole genome microarray Affymetrix Human U133 plus 2.0 was used to obtain the raw data followed by normalization, summarization and background adjustments by means of Robust Multichip Average Express software. Raw data of the different conditions were included as .CEL files in the Gene Expression Omnibus with accession number GSE169072. These data may serve as the basis for further refinement studies to establish an adequate transcriptomic signature of chemical-induced cholestasis fit-for-purpose in screening the cholestatic liability of different types of chemical compounds.

Acid-sensing ion channels modulate bladder nociception.

Sensitization of neuronal pathways and persistent afferent drive are major contributors to somatic and visceral pain. However, the underlying mechanisms that govern whether afferent signaling will give rise to sensitization and pain are not fully understood. In the present report, we investigated the contribution of acid-sensing ion channels (ASICs) to bladder nociception in a model of chemical cystitis induced by cyclophosphamide (CYP). We found that the administration of CYP to mice lacking ASIC3, a subunit primarily expressed in sensory neurons, generates pelvic allodynia at a time point at which only modest changes in pelvic sensitivity are apparent in wild-type mice. The differences in mechanical pelvic sensitivity between wild-type and Asic3 knockout mice treated with CYP were ascribed to sensitized bladder C nociceptors. Deletion of Asic3 from bladder sensory neurons abolished their ability to discharge action potentials in response to extracellular acidification. Collectively, the results of our study support the notion that protons and their cognate ASIC receptors are part of a mechanism that operates at the nerve terminals to control nociceptor excitability and sensitization.NEW & NOTEWORTHY Our study indicates that protons and their cognate acid-sensing ion channel receptors are part of a mechanism that operates at bladder afferent terminals to control their function and that the loss of this regulatory mechanism results in hyperactivation of nociceptive pathways and the development of pain in the setting of chemical-induced cystitis.

Chemical-induced aseptic meningitis as a result of intrathecal hydromorphone therapy: Case report.

Chemical meningitis, though rare, is a diagnosis of exclusion that must be considered in patients presenting with neurologic symptoms of undetermined cause. It is likely that any substance in contact with CSF can be the culprit.

In silico prediction of chemical-induced hematotoxicity with machine learning and deep learning methods.

Chemical-induced hematotoxicity is an important concern in the drug discovery, since it can often be fatal when it happens. It is quite useful for us to give special attention to chemicals which can cause hematotoxicity. In the present study, we focused on in silico prediction of chemical-induced hematotoxicity with machine learning (ML) and deep learning (DL) methods. We collected a large data set contained 632 hematotoxic chemicals and 1525 approved drugs without hematotoxicity. Computational models were built using several different machine learning and deep learning algorithms integrated on the Online Chemical Modeling Environment (OCHEM). Based on the three best individual models, a consensus model was developed. It yielded the prediction accuracy of 0.83 and balanced accuracy of 0.77 on external validation. The consensus model and the best individual model developed with random forest regression and classification algorithm (RFR) and QNPR descriptors were made available at https://ochem.eu/article/135149 , respectively. The relevance of 8 commonly used molecular properties and chemical-induced hematotoxicity was also investigated. Several molecular properties have an obvious differentiating effect on chemical-induced hematotoxicity. Besides, 12 structural alerts responsible for chemical hematotoxicity were identified using frequency analysis of substructures from Klekota-Roth fingerprint. These results should provide meaningful knowledge and useful tools for hematotoxicity evaluation in drug discovery and environmental risk assessment.

Chimeric Mouse With Humanized Liver Is an Appropriate Animal Model to Investigate Mode of Action for Porphyria-Mediated Hepatocytotoxicity.

Porphyrinogenic compounds are known to induce porphyria-mediated hepatocellular injury and subsequent regenerative proliferation in rodents, ultimately leading to hepatocellular tumor induction. However, an appropriate in vivo experimental model to evaluate an effect of porphyrinogenic compounds on human liver has not been fully established. Recently, the chimeric mouse with humanized liver (PXB mice) became widely used as a humanized model in which human hepatocytes are transplanted. In the present study, we examined the utility of PXB mice as an in vivo experimental model to evaluate the key events of the porphyria-mediated cytotoxicity mode of action (MOA) in humans. The treatment of PXB mice with 5-aminolevulinic acid, a representative porphyrinogenic compound, for 28 days caused protoporphyrin IX accumulation, followed by hepatocyte necrosis, increased mitosis, and an increase in replicative DNA synthesis in human hepatocytes, indicative of cellular injury and regenerative proliferation, similar to findings in patients with porphyria or experimental porphyria models and corresponding to the key events of the MOA for porphyria-mediated hepatocellular carcinogenesis. We conclude that the PXB mouse is a useful model to evaluate the key events of the porphyria-mediated cytotoxicity MOA in humans and suggest the utility of PXB mice for clarifying the human relevancy of findings in mice.

Extracting chemical-induced disease relation by integrating a hierarchical concentrative attention and a hybrid graph-based neural network.

Extracting the chemical-induced disease relation from literatures is important for biomedical research. On one hand, it is challenging to capture the interactions among remote words and the long-distance information is not adequately exploited by existing systems for document-level relation extraction. On the other hand, there is some information particularly important to the target relations in documents, which should attract more attention than the less relevant information for the relation extraction. However, this issue is not well addressed in existing methods. In this paper, we present a method that integrates a hybrid graph and a hierarchical concentrative attention to overcome these problems. The hybrid graph is constructed by synthesizing the syntactic graph and Abstract Meaning Representation graph to acquire the long-distance information for document-level relation extraction. Meanwhile, the concentrative attention is used to focus on the most important information, and alleviate the disturbance brought by the less relevant items in the document. The experimental results demonstrate that our model yields competitive performance on the dataset of chemical-induced disease relations.

Induced proximity tools for precise manipulation of lipid signaling.

Lipids are highly dynamic molecules that, due to their hydrophobicity, are spatially confined to membrane environments. From these locations, certain privileged lipids serve as signaling molecules. For understanding the biological functions of subcellular pools of signaling lipids, induced proximity tools have been invaluable. These methods involve controlled heterodimerization, by either small-molecule or light triggers, of functional proteins. In the arena of lipid signaling, induced proximity tools can recruit lipid-metabolizing enzymes to manipulate lipid signaling and create artificial tethers between organelle membranes to control lipid trafficking pathways at membrane contact sites. Here, we review recent advances in methodology development and biological application of chemical-induced and light-induced proximity tools for manipulating lipid metabolism, trafficking, and signaling.

CID-GCN: An Effective Graph Convolutional Networks for Chemical-Induced Disease Relation Extraction.

Automatic extraction of chemical-induced disease (CID) relation from unstructured text is of essential importance for disease treatment and drug development. In this task, some relational facts can only be inferred from the document rather than single sentence. Recently, researchers investigate graph-based approaches to extract relations across sentences. It iteratively combines the information from neighbor nodes to model the interactions in entity mentions that exist in different sentences. Despite their success, one severe limitation of the graph-based approaches is the over-smoothing problem, which decreases the model distinguishing ability. In this paper, we propose CID-GCN, an effective Graph Convolutional Networks (GCNs) with gating mechanism, for CID relation extraction. Specifically, we construct a heterogeneous graph which contains mention, sentence and entity nodes. Then, the graph convolution operation is employed to aggregate interactive information on the constructed graph. Particularly, we combine gating mechanism with the graph convolution operation to address the over-smoothing problem. The experimental results demonstrate that our approach significantly outperforms the baselines.

A review of species differences in the control of, and response to, chemical-induced thyroid hormone perturbations leading to thyroid cancer.

This review summarises the current state of knowledge regarding the physiology and control of production of thyroid hormones, the effects of chemicals in perturbing their synthesis and release that result in thyroid cancer. It does not consider the potential neurodevelopmental consequences of low thyroid hormones. There are a number of known molecular initiating events (MIEs) that affect thyroid hormone synthesis in mammals and many chemicals are able to activate multiple MIEs simultaneously. AOP analysis of chemical-induced thyroid cancer in rodents has defined the key events that predispose to the development of rodent cancer and many of these will operate in humans under appropriate conditions, if they were exposed to high enough concentrations of the affecting chemicals. There are conditions however that, at the very least, would indicate significant quantitative differences in the sensitivity of humans to these effects, with rodents being considerably more sensitive to thyroid effects by virtue of differences in the biology, transport and control of thyroid hormones in these species as opposed to humans where turnover is appreciably lower and where serum transport of T4/T3 is different to that operating in rodents. There is heated debate around claimed qualitative differences between the rodent and human thyroid physiology, and significant reservations, both scientific and regulatory, still exist in terms of the potential neurodevelopmental consequences of low thyroid hormone levels at critical windows of time. In contrast, the situation for the chemical induction of thyroid cancer, through effects on thyroid hormone production and release, is less ambiguous with both theoretical, and actual data, showing clear dose-related thresholds for the key events predisposing to chemically induced thyroid cancer in rodents. In addition, qualitative differences in transport, and quantitative differences in half life, catabolism and turnover of thyroid hormones, exist that would not operate under normal situations in humans.

Solving Gravimetric-Volumetric Capacitive Paradox of 2D Materials through Dual-Functional Chemical Bonding-Induced Self-Constructing Graphene-MXene Monoliths.

High electrical conductivity and all-open microstructure characteristics intrinsically endow both graphene and MXenes with superior electrochemical energy storage capability. However, the above two-dimensional (2D) thicker electrodes (>20 µm) severely dilute their unique rapid electronic-ionic transferring characteristic, posing a paradox of high gravimetric and high volumetric capacitive properties due to massively excessive macropores or an unduly restacked issue. Herein, we elaborately construct novel monolithic NH2-graphene and Ti3C2Tx MXene (NG@MX) composites through dual-functional induced self-assembly with the help of both covalent and hydrogen bonding interactions. Notably, much thicker monolithic NG@MX electrodes (>90 µm) fabricated by a conventional roll-coating method without any further compaction treatment can simultaneously deliver two times gravimetric (gra.) and volumetric (vol.) performance than those of pure graphene (in vol.) or MXene (in gra.) materials. Moreover, monolithic NG@MX-based supercapacitors can remarkably present two times energy density as that of graphene and four times as MXene, respectively. Such greatly enhanced electrochemical properties are closely related to the appropriate equilibrium of the volumetric density and the open structure, which can effectively guarantee the rapid transfer of both electrons and ions in the thick monolithic NG@MX electrodes. Undoubtedly, dual-functional chemical bonding-induced self-constructing NG@MX monoliths efficiently solve the long-existing gra. and vol. capacitive paradox of the thicker 2D materials used in supercapacitors, which will guide the design of high-performance capacitive materials and promote their practical application in electrochemical energy storage.

Regulation of the NLRP3 inflammasome with natural products against chemical-induced liver injury.

The past decades have witnessed significant progress in understanding the process of sterile inflammation, which is dependent on a cytosolic complex termed the nucleotide-binding oligomerization domain (NOD)-like receptor containing pyrin domain 3 (NLRP3) inflammasome. Activation of NLRP3 inflammasome requires two steps, including the activation of Toll-like receptor (TLR) by its ligands, resulting in transcriptional procytokine and inflammasome component activation, and the assembly and activation of NLRP3 inflammasome triggered by various danger signals, leading to caspase-1 activation, which could subsequently cleave procytokines into their active forms. Metabolic disorders, ischemia and reperfusion, viral infection and chemical insults are common pathogenic factors of liver-related diseases that usually cause tissue damage and cell death, providing numerous danger signals for the activation of NLRP3 inflammasome. Currently, natural products have attracted much attention as potential agents for the prevention and treatment of liver diseases due to their multitargets and nontoxic natures. A great number of natural products have been shown to exhibit beneficial effects on liver injury induced by various chemicals through regulating NLRP3 inflammasome pathways. In this review, the roles of the NLRP3 inflammasome in chemical-induced liver injury (CILI) and natural products that exhibit beneficial effects in CILI through the regulation of inflammasomes were systematically summarized.